PDBsum entry: 1f0v

Hydrolase/DNA

PDB id: 1f0v

Contents

Protein chains

124 a.a. *

Ligands

_DC-_DG ×4

PO4 ×4

GOL ×24

Waters ×554

* Residue conservation analysis

PDB id:

1f0v

Name:

Hydrolase/DNA

Title:

Crystal structure of an rnase a dimer displaying a new type domain swapping

Structure:

5'-d( Cp G)-3'. Chain: m, n, o, p. Engineered: yes. Ribonuclease a. Chain: a, b, c, d. Synonym: rnase 1, rnase a. Ec: 3.1.27.5

Source:

Synthetic: yes. Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas

Biol. unit:

Tetramer (from PQS)

Resolution:

1.70Å R-factor: 0.184 R-free: 0.213

Authors:

Y.S.Liu,G.Gotte,M.Libonati,D.S.Eisenberg

Key ref:

Y.Liu et al. (2001). A domain-swapped RNase A dimer with implications for amyloid formation. Nat Struct Biol, 8, 211-214. PubMed id: 11224563 DOI: 10.1038/84941

Date:

17-May-00 Release date: 21-Feb-01

Protein chains

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic

Seq: 150 a.a.

Struc: 124 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.27.5 - Pancreatic ribonuclease.
• Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biochemical function: nucleic acid binding (6 terms)

DOI no: 10.1038/84941

Nat Struct Biol 8:211-214 (2001)

PubMed id: 11224563

A domain-swapped RNase A dimer with implications for amyloid formation.

Y.Liu, G.Gotte, M.Libonati, D.Eisenberg.

ABSTRACT

Bovine pancreatic ribonuclease (RNase A) forms two types of dimers (a major and a minor component) upon concentration in mild acid. These two dimers exhibit different biophysical and biochemical properties. Earlier we reported that the minor dimer forms by swapping its N-terminal alpha-helix with that of an identical molecule. Here we find that the major dimer forms by swapping its C-terminal beta-strand, thus revealing the first example of three-dimensional (3D) domain swapping taking place in different parts of the same protein. This feature permits RNase A to form tightly bonded higher oligomers. The hinge loop of the major dimer, connecting the swapped beta-strand to the protein core, resembles a short segment of the polar zipper proposed by Perutz and suggests a model for aggregate formation by 3D domain swapping with a polar zipper.

Selected figure(s)

Figure 1.
Figure 1. Ribbon diagrams of the structures of RNase A. a, The monomer26; b, the minor dimer3; c, the major dimer (this paper); and d, a model of a trimer of (a) produced by combining panels (b) and (c). The N- and C-termini are labeled. In the minor dimer the N-terminal -helices are swapped, whereas in the major dimer, the C-terminal -strands are swapped. The closed interfaces are the interface between the blue segment and the green core structure, and the interface between the red segment and the green core structure in (a), which are also found in the minor dimer (b) and the major dimer (c), respectively. The open interface in the minor dimer lies between the green and the blue strands in the middle of the -sheet in (b), and the open interface in the major dimer lies between the red and the green segments in the center of the molecule in (c). These open interfaces do not exist in (a). The core domain of the green subunit in each molecule has the same orientation. In the model of the trimer, domain swapping takes place at both the N- and C-termini. The figure was created using Raster3D^29.

Figure 2.
Figure 2. Stereo view of the 2F[o] - F[c] electron density map of the inhibitor of RNase A, dCpdG, contoured at 1.4 to illustrate its detail. The stick model of dCpdG is shown in green. The figure is plotted with the progrem O27.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 211-214) copyright 2001.

Figures were selected by an automated process.